Figure 1. GeneSiDer user personal homepage

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Mae Stevenson
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The GeneSiDer sodware by Geospiza will streamline our procedures and provide our users with an enhanced service, including tracking of orders and samples, sequence visualisa?

1 Sanger Sequencing and GeneMapper Services at The GenePool The GenePool will be introducing a new Laboratory Informa?on Management System (LIMS) for submission, processing and accessing of Sanger sequencing samples. The GeneSiDer sodware by Geospiza will streamline our procedures and provide our users with an enhanced service, including tracking of orders and samples, sequence visualisa?on and an online sequence management tool. This document is a step- by- step guide to help you navigate GeneSiDer. We have created accounts for Principal Inves?gators who have used the service in the last 12 months. We have ed you enclosing your account details. We strongly recommend that you change your password ader logging in for the first?me at hlp://genepool- lims1.bio.ed.ac.uk/ To change your password, click on your username at the top right of your GeneSiDer homepage. Click on Edit User and enter your new password. We have asked PIs to tell us of the staff members they wish to have a GeneSiDer account and once we receive this informa?on we will create accounts for these staff members and them with their account details. Figure 1. GeneSiDer user personal homepage Figure 1 shows a user s personal homepage. On the right are two dashboards, one showing the number of orders you have made and their status. The second dashboard is a summary of your data showing the number of folders and projects you can access and how many chromatograms and fragment analysis files you can view. On the led is a menu used to navigate your orders and data. TO PLACE AN ORDER Click on Place Order in the led hand menu of your homepage. Choose an order form depending on which service you require. Note that there are different order forms for TUBE and PLATE sample submission. The services are Sequencer only for tubes, Sequencer only for plates, Big Dye reac?on required for tubes, Big Dye reac?on required for plates, GeneMapper plates and GeneMapper for half plates.

Figure 2. Choose an order form for the service you require Click on the service you require and this will take you to the order form for that par?cular service. If you require mul?

2 Figure 2. Choose an order form for the service you require Click on the service you require and this will take you to the order form for that par?cular service. If you require mul?ple services you will need to make mul?ple orders using the specific order form for each service. Figure 3. Order form for Sequencer only for plates service Figure 3. Order Informa?on Choose a Project that you would like your data to be assigned to. The default op?on will place your data in an auto- generated Project named ader your username e.g. Sanger_customer. The order name is auto- generated by GeneSiDer. Press Next. Note that required fields are denoted with a red star.

Throughout GeneSiDer you will find blue ac?on bulons at the top of a page. Click on these to carry out the labelled func?ons. For example, to delete an order.

Before your order can be submiled, you are required to enter your purchasing informa?on and add samples to your order. Figure 4.

3 Throughout GeneSiDer you will find blue ac?on bulons at the top of a page. Click on these to carry out the labelled func?ons. For example, to delete an order. The order details page shows customer and order informa?on already submiled. You can edit the order by clicking on the blue Edit Order bulon. Before your order can be submiled, you are required to enter your purchasing informa?on and add samples to your order. Figure 4. Order Details page ADDING PURCHASING INFORMATION Please select your PI name and address in the BILL TO dropdown menu. If their details are not there, add them using the ADD ADDRESS link. This is required for Invoicing. Enter your own address in the SHIP TO dropdown menu. If your details are not there or require edi?ng, add them using the ADD ADDRESS link. You will only need to do this once. Figure 5. Purchasing informa?on page Enter your charge code number depending on where your funding is held. See Figure 6 to decide which type of charge code you are required to enter.

Charge Code Type Cost Centre & Grant Number eit Number NBAF Number Descrip?on For University of Edinburgh, School of Biological Sciences users only.

4 Charge Code Type Cost Centre & Grant Number eit Number NBAF Number Descrip?on For University of Edinburgh, School of Biological Sciences users only. Valid format is CostCentre_GrantNumber where CostCentre consists of three digits and three capital lelers and GrantNumber usually consists of one leler followed by digits. For University of Edinburgh users OUTWITH the School of Biological Sciences only. For NERC/NBAF users only. NBAF numbers are included in the award leler sent by NBAF following a successful applica?on Purchase Order Number Figure 6. Charge code types For all users outside the University of Edinburgh. Please provide a purchase order number here and also upload the purchase order form on the Order form. ADDING SAMPLE INFORMATION For PLATE Orders Enter the name of your plate here. Enter the first sample name in the Sample box and use the Easy fill controls to enter your other sample names. Easy fill controls Figure 7. Adding samples (by plate) See Figure 8 for how to use the Easy Fill controls For TUBE Orders Note that on Order forms for sample submission by TUBE, sample informa?on is entered alongside the order informa?on. If you are submihng more than 24 samples, click on More Rows at the bolom of the form to show more sample name fields. This will give 24 more fields each?me More Rows is clicked, up to a maximum of 88 samples. It is more economical for you to submit more than 88 samples as a plate order.

5 Fills every row in the selected range with the same informa?on Checks if you ended your entry with a number. If so, Fill Down Plus will create a unique string for each row by incremen?ng the last number in your entry by one. Deletes all informa?on in the column Locks all other rows so you can use the tab key to move to the next row in the highlighted column Specifies the range of rows the easy fill control will affect. For example, 6-8, 12 will present rows 6,7,8 and 12. And A01- H01 will present the first column Downloads the en?re Sample Informa?on grid as an Excel document Allows the user to browse to the loca?on of the saved Excel document Figure 8. Easy fill controls You can also input your Sample names using the Excel download and upload bulons. Click on the Excel download bulon. This downloads an excel file named GeneSiDer_InputGrid.xls. Fill this in with your sample names and SAVE it to your computer. Click on the Excel Upload bulon, browse to the saved file and click the upload bulon. Your sample names will now be in GeneSiDer. When you have entered the sample names click on Next and return to the order details page. To make changes to the order use the blue ac?on bulons at the top of the page, Edit order or Edit Purchasing Informa?on To delete the order click on Delete Order To add another plate of samples to your order click on Add Sample Plate WHEN YOU ARE HAPPY WITH THE ORDER CLICK ON SUBMIT ORDER. SUBMITTING YOUR SAMPLES TO THE GENEPOOL Open the order you just created, make a PDF by clicking on the blue PDF bulon at the top of the page and print the PDF. Place your samples along with the PDF printout in the GenePool labelled bags. Please ensure that your samples are properly sealed, packaged and labelled with the Order Number as generated by GeneSiDer.

EMAIL CONFIRMATION You will receive an email confirming your order.

6 CONFIRMATION You will receive an confirming your order. s will also be sent if there is a problem with your order, when your samples begin processing in the lab and when your results are ready to view. VIEWING YOUR ORDERS You can view the progress of your orders at any?me by clicking View orders in the led hand menu. To enable you to quickly navigate to your required order/folder/chromatogram etc., GeneSiDer has Find bars. Type your request in the text box and choose what you want to search (e.g. order name, order type etc) and by what method (e.g. contains, does not contain, is, starts with, etc) from the dropdown menus. Figure 9. Viewing Orders page with Find bar highlighted Order Name: click on an order to take you to the Order Details page. Order Type: which service was ordered. Project: shows which Project the order data folder is kept in. Click on a Project to take you to that Project, showing all the data folders it contains. Status: New orders have yet to be submiled. All submiled orders will be In review un?l the Sanger Team start Processing them in the lab. When an order is Completed click on it to take you to the data folder. Owner: who made the order. Created At:?me and date of order crea?on.

Figure 10. File architecture within GeneSiDer Folders are auto- generated by GeneSiDer for each order and all data from that order will be stored here.

7 Figure 10. File architecture within GeneSiDer Folders are auto- generated by GeneSiDer for each order and all data from that order will be stored here. Folders are organised into Projects (Projects can be Researcher name or by Research topic etc) and you may create different Projects to organise your data. You can choose which Project to store your data folder in when crea?ng an order. The default op?on will place the data folder in an auto- generated Project named ader your username e.g. Researcher A. Folders can be moved between Projects. Projects from users within one Lab group will be accessible to all other members of the Lab group.

ACCESSING YOUR DATA Navigate to folders and Projects through the dashboard or the Data menu on your GeneSiDer homepage via View Folders or View Projects. Figure 11.

ve or Inac?ve within the Edit folder page. To view your data, click on the folder name.

8 ACCESSING YOUR DATA Navigate to folders and Projects through the dashboard or the Data menu on your GeneSiDer homepage via View Folders or View Projects. Figure 11. View Folders page The View Folders page shows a list of your folders and a summary of the data they contain. There are tabs to view Ac?ve, Inac?ve and All folders. You can set folders to be Ac?ve or Inac?ve within the Edit folder page. To view your data, click on the folder name. You will find chromatograms, the sequence length, trimmed sequence length, quality scores and signal strengths here. Figure 12. Viewing contents of folder Use the blue ac?on bulons at the top of the Folder contents page to edit folders, relabel the chromatograms, move the chromatograms to another folder, download the chromatograms or to view the Folder Report.

EDITING FOLDERS Click on the blue Edit Folder ac?on bulon at the top of the page to edit a folder. You can also move a folder to a different project by edi?ng the folder. Figure 13.

9 EDITING FOLDERS Click on the blue Edit Folder ac?on bulon at the top of the page to edit a folder. You can also move a folder to a different project by edi?ng the folder. Figure 13. Edit Folders The Magnifying glass icon opens a window lis?ng the choices on offer. Click on your choice to populate the Project field. The magnifying glass feature is used throughout GeneSiDer for choosing from a list of op?ons. RELABEL ALL CHROMATS Figure 14. Relabel chromatograms MOVE ALL CHROMATS Chromatograms may be moved to a new folder by clicking the blue Move all chromats ac?on bulon and choosing a des?na?on folder.

DOWNLOAD ALL CHROMATS Op?ons for downloading chromatograms: All Chromatograms with trace data Chromatograms with basecalls All Chromatograms. You also have the op?on of conver?ng AB1 to SCF format.

10 DOWNLOAD ALL CHROMATS Op?ons for downloading chromatograms: All Chromatograms with trace data Chromatograms with basecalls All Chromatograms. You also have the op?on of conver?ng AB1 to SCF format. Choose from one file with mul?ple sequences or many files in one folder. Op?on of downloading Phd files Figure 15. Download chromatograms We recommend you choose All chromatograms from the first dropdown menu and click on Download Chromats. This will download a file named Folder_name_chromats.zip to your computer for you to view using your normal sequence viewer. To download a folder of sequence files (Folder_name_sequences.zip),?ck the Nucleo?des box and choose Many files in folder from the Format dropdown menu. You can also download one file containing all the sequences (nucleo?des.fasta), a quality file (quality_scores.qual) and transla?ons (transla?ons.txt). FOLDER REPORT The folder report details quality sta?s?cs, quality plots and a Q20 histogram of all sequences in the folder. You can click on the sequence name to view the chromatogram (see Figure 17). Click on the icon to the led of the sequence name to view the sequence in FinchTV, GeneSiDer s trace viewer. Figure 16. Folder Report

11 VIEWING CHROMATOGRAMS View the chromatograms in GeneSiDer by clicking on the chromat in the Contents of folder page or in Folder report page. If you download the chromatograms, you can view them using your usual trace viewer or download FinchTV from the Get FinchTV link at the top right of any page. Figure 17. Chromatogram read If you have any ques?ons, please do not hesitate to contact us at genepool- Website: hlp://genepool.bio.ed.ac.uk/ FAQs: hlp://genepool.bio.ed.ac.uk/sanger/sangerfaq.html Troubleshoo?ng: hlp://genepool.bio.ed.ac.uk/sanger/sanger_troubleshoo?ng_guide_v1.pdf

Nevada Genomics Center

Nevada Genomics Center These are general instructions on how to use dnatools to submit Sanger sequencing samples to be run on the ABI Prism 3730 DNA analyzer. We here at the Nevada Genomics Center feel